| | HIV protein | AA position | HLA | Sequence | Clade |
| | gp160 | 2–10 | B*0801 (B8) | RVKEKYQHL | — | | gp160 | 31–39 | B*1801 (B18) | AENLWVTVY | B | | gp160 | 31–39 | B44 | AENLWVTVY | B | | gp160 | 31–40 | B*4402 (B44) | AENLWVTVYY | — | | gp160 | 37–46 | A*0301 (A3) | TVYYGVPVWK | A, B, C, D | | gp160 | 42–51 | B*5501 (B55) | VPVWKEATTT | — | | gp160 | 42–52 | B*3501 (B35) | VPVWKEATTTL | B | | gp160 | 52–61 | A*2402 (A24) | LFCASDAKAY | — | | gp160 | 59–69 | B58 | KAYETEVHNVW | C | | gp160 | 61–69 | B*1801 (B18) | YETEVHNVW | B | | gp160 | 78–86 | B*3501 (B35) | DPNPQEVVL | B | | gp160 | 104–112 | B*3801 (B38) | MHEDIISLW | B | | gp160 | 199–207 | A*1101 (A11) | SVITQACPK | B | | gp160 | 209–217 | A*2902 (A29) | SFEPIPIHY | B, D | | gp160 | 298–307 | B*0702 (B7) | RPNNNTRKSI | B, C | | gp160 | 310–318 | A*3002 (A30) | HIGPGRAFY | B | | gp160 | 311–320 | A*0201 (A2) | RGPGRAFVTI | A, B, C | | gp160 | 375–383 | B*1516 (B63) | SFNCGGEFF | A, B, C | | gp160 | 375–383 | Cw*0401 (Cw4) | SFNCGGEFF | A, B, C | | gp160 | 416–424 | B*5101 (B51) | LPCRIKQII | B | | gp160 | 419–427 | A*3201 (A32) | RIKQIINMW | B, C | | gp160 | 511–519 | Cw18 | YRLGVGALI | C | | gp160 | 557–565 | Cw*0304 (Cw10) | RAIEAQQHL | A, B, C, D | | gp160 | 557–565 | Cw8 | RAIEAQQHM | A, B, C, D | | gp160 | 557–565 | Cw15 | RAIEAQQHL | C | | gp160 | 584–592 | B*1402 (B14) | ERYLKDQQL | A, B, C, D | | gp160 | 585–593 | A23 | RYLKDQQLL | B, C | | gp160 | 585–593 | A*2402 (A24) | RYLKDQQLL | B, C | | gp160 | 586–593 | B*0801 (B8) | YLKDQQLL | A, B | | gp160 | 606–614 | B*3501 (B35) | TAVPWNASW | B | | gp160 | 698–707 | A*3303 (A33) | VFAVLSIVNR | B | | gp160 | 703–712 | A*2501 (A25) | EIIFDIRQAY | — | | gp160 | 704–712 | A*3002 (A30) | IVNRNRQGY | B | | gp160 | 770–780 | A*0301 (A3) | RLRDLLLIVTR | B, C | | gp160 | 770–780 | A*3101 (A31) | RLRDLLLIVTR | B, C | | gp160 | 777–785 | A*6802 (A68) | IVTRIVELL | B | | gp160 | 786–795 | B*2705 (B27) | GRRGWEALKY | B | | gp160 | 787–795 | A*0101 (A1) | RRGWEVLKY | B | | gp160 | 794–802 | A*3002 (A30) | KYCWNLLQY | B | | gp160 | 805–814 | B*4001 (B60) | QELKNSAVSL | B | | gp160 | 813–822 | A*0201 (A2) | SLLNATDIAV | B | | gp160 | 831–838 | A*3303 (A33) | EVAQRAYR | B | | gp160 | 843–851 | B*0702 (B7) | IPRRIRQGL | A, B, C, D | | gp160 | 846–854 | A*0205 (A2) | RIRQGLERA | B | | gp160 | 848–856 | B8 | RQGLERALL | — | | Integrase | 28–36 | B42 | LPPIVAKEI | B, C | | Integrase | 66–74 | B*1510 (B71) | THLEGKIIL | B, C | | Integrase | 123–132 | B57 | STTVKAACWW | B | | Integrase | 135–143 | B*1503 (B72) | IQQEFGIPY | B, C | | Integrase | 165–172 | Cw18 | VRDQAEHL | C | | Integrase | 173–181 | B*5701 (B57) | KTAVQMAVF | B | | Integrase | 179–188 | A*0301 (A3) | AVFIHNFKRK | B, multiple | | Integrase | 179–188 | A*1101 (A11) | AVFIHNFKRK | B, multiple | | Integrase | 185–194 | B*1503 (B72) | FKRKGGIGGY | B, C | | Integrase | 203–211 | A*1101 (A11) | IIATDIQTK | B | | Integrase | 219–227 | A*3002 (A30) | KIQNFRVYY | AE, B, C, D | | Integrase | 260–268 | B42 | VPRRKAKII | — | | Integrase | 263–271 | B*1503 (B72) | RKAKIIRDY | B, C | | Nef | 13–20 | B*0801 (B8) | WPTVRERM | B | | Nef | 19–27 | B62 | RMRRAEPAA | B | | Nef | 37–45 | B*4001 (B60) | LEKHGAITS | B | | Nef | 37–45 | B50 | LEKHGAITS | B | | Nef | 68–76 | B*0702 (B7) | FPVTPQVPL | B | | Nef | 68–77 | B*0702 (B7) | FPVTPQVPLR | B | | Nef | 71–79 | B*0702 (B7) | TPQVPLRPM | B | | Nef | 71–79 | B*4201 (B42) | RPQVPLRPM | B, C | | Nef | 73–82 | A*0301 (A3) | QVPLRPMTYK | A, B, C, D | | Nef | 73–82 | A*1101 (A11) | QVPLRPMTYK | A, B, C, D | | Nef | 74–81 | B*3501 (B35) | VPLRPMTY | A, B, C, D | | Nef | 75–82 | A*1101 (A11) | PLRPMTYK | B | | Nef | 77–85 | B*0702 (B7) | RPMTYKAAL | B | | Nef | 82–91 | Cw8 | KAAVDLSHFL | B | | Nef | 83–91 | A*0205 (A2) | GAFDLSFFL | A | | Nef | 83–91 | Cw3 | AALDLSHFL | B | | Nef | 83–91 | Cw*0802 (Cw8) | AAVDLSHFL | B, C | | Nef | 84–92 | A*0301 (A3) | AVDLSHFLK | A, B, D, F | | Nef | 84–92 | A*1101 (A11) | AVDLSHFLK | A, B, D, F | | Nef | 90–97 | B*0801 (B8) | FLKEKGGL | A, B, C, D | | Nef | 92–100 | B*4001 (B60) | KEKGGLEGL | B, C | | Nef | 92–100 | B*4002 (B61) | KEKGGLEGL | B, C | | Nef | 105–114 | B*2705 (B27) | RRQDILDLWI | B | | Nef | 105–115 | B18 | RRQDILDLWVY | B | | Nef | 105–115 | Cw7 | KRQEILDLWVY | B, C | | Nef | 106–114 | B13 | RQDILDLWI | B | | Nef | 106–115 | B*0702 (B7) | RQDILDLWIY | — | | Nef | 116–124 | B57 | HTQGYFPDW | B, C | | Nef | 116–125 | B*5701 (B57) | HTQGYFPDWQ | B, C | | Nef | 117–127 | B*1501 (B62) | TQGYFPDWQNY | B, C | | Nef | 120–128 | A29 | YFPDWQNYT | B, C | | Nef | 120–128 | B*3701 (B37) | YFPDWQNYT | B, C | | Nef | 120–128 | B*5701 (B57) | YFPDWQNYT | B, C | | Nef | 120–128 | Cw6 | YFPDWQNYT | B, C | | Nef | 127–135 | B57 | YTPGPGIRY | B, C | | Nef | 127–135 | B63 | YTPGPGIRY | B, C | | Nef | 128–137 | B*0702 (B7) | TPGPGVRYPL | B, C | | Nef | 128–137 | B*4201 (B42) | TPGPGVRYPL | B, C | | Nef | 133–141 | A33 | TRYPLTFGW | B | | Nef | 134–141 | A*2402 (A24) | RYPLTFGW | B, C | | Nef | 135–143 | B*1801 (B18) | YPLTFGWCY | B, C, D | | Nef | 135–143 | B53 | YPLTFGWCF | B | | Nef | 135–143 | B*5301 (B53) | YPLTFGWCY | B | | Nef | 136–145 | A*0201 (A2) | PLTFGWCYKL | B | | Nef | 137–145 | B57 | LTFGWCFKL | A, B, C | | Nef | 137–145 | B63 | LTFGWCFKL | A, B, C | | Nef | 180–189 | A*0201 (A2) | VLEWRFDSRL | B | | Nef | 183–191 | B*1503 (B72) | WRFDSRLAF | B | | p17 | 11–19 | B*4002 (B61) | GELDRWEKI | B | | p17 | 18–26 | A*0301 (A3) | KIRLRPGGK | A, B | | p17 | 19–27 | B*2705 (B27) | IRLRPGGKK | B | | p17 | 20–28 | A*0301 (A3) | RLRPGGKKK | A, B | | p17 | 20–29 | A*0301 (A3) | RLRPGGKKKY | B | | p17 | 24–32 | B*0801 (B8) | GGKKKYKLK | B, F | | p17 | 28–36 | A*2402 (A24) | KYKLKHIVW | B, C, F | | p17 | 33–41 | Cw*0804 (Cw8) | HLVWASREL | C | | p17 | 34–44 | A30 | LVWASRELERF | B, C | | p17 | 36–44 | B*3501 (B35) | WASRELERF | B, C | | p17 | 74–82 | B*0801 (B8) | ELRSLYNTV | F | | p17 | 76–86 | A*3002 (A30) | RSLYNTVATLY | B, C, F | | p17 | 76–86 | B58 | RSLYNTVATLY | B, C, F | | p17 | 76–86 | B63 | RSLYNTVATLY | B, C, F | | p17 | 77–85 | A*0201 (A2) | SLYNTVATL | A, B, C, D, F, G, K | | p17 | 77–85 | A*0202 (A2) | SLYNTVATL | A, B, C, D, F, G, K | | p17 | 77–85 | A*0205 (A2) | SLYNTVATL | A, B, C, D, F, G, K | | p17 | 78–85 | Cw14 | LYNTVATL | B, D | | p17 | 78–86 | A*2902 (A29) | LYNTVATLY | B, C | | p17 | 78–86 | B*4403 (B44) | LYNTVATLY | B, C | | p17 | 84–91 | A*1101 (A11) | TLYCVHQK | — | | p17 | 92–101 | B*4001 (B60) | IEIKDTKEAL | B, F | | p17 | 124–132 | B*3501 (B35) | NSSKVSQNY | B | | p24 | 3–11 | B13 | VQNLQGQMV | B, C | | p24 | 12–20 | B*1510 (B71) | HQAISPRTL | B | | p24 | 13–23 | A*2501 (A25) | QAISPRTLNAW | B | | p24 | 15–23 | B*5701 (B57) | ISPRTLNAW | A, C | | p24 | 15–23 | B63 | ISPRTLNAW | A, B, C, D | | p24 | 16–24 | B*0702 (B7) | SPRTLNAWV | B | | p24 | 24–32 | B*1503 (B72) | VKVIEEKAF | B, C | | p24 | 28–36 | B*4415 (B12) | EEKAFSPEV | A, B, C, D | | p24 | 30–37 | B*5703 (B57) | KAFSPEVI | B | | p24 | 30–40 | B*5701 (B57) | KAFSPEVIPMF | A, B, C, G | | p24 | 30–40 | B*5703 (B57) | KAFSPEVIPMF | A, B, C, G | | p24 | 30–40 | B63 | KAFSPEVIPMF | A, B, C, G | | p24 | 32–40 | B57 | FSPEVIPMF | B, C | | p24 | 35–43 | A*2601 (A26) | EVIPMFSAL | A, B, C, D | | p24 | 36–43 | Cw*0102 (Cw1) | VIPMFSAL | B, D | | p24 | 44–52 | B*4001 (B60) | SEGATPQDL | B | | p24 | 48–56 | B*0702 (B7) | TPQDLNTML | A, B, C, D | | p24 | 48–56 | B*3910 (B39) | TPQDLNTML | A, B, C, D | | p24 | 48–56 | B*4201 (B42) | TPQDLNTML | A, B, C, D | | p24 | 48–56 | B*5301 (B53) | TPYDINQML | A | | p24 | 48–56 | B*8101 (B81) | TPQDLNTML | A, B, C, D | | p24 | 48–56 | Cw*0802 (Cw8) | TPQDLNTML | A, B, C, D | | p24 | 61–69 | B*1510 (B71) | GHQAAMQML | B, C | | p24 | 61–69 | B*3901 (B39) | GHQAAMQML | B, C | | p24 | 70–78 | B*4002 (B61) | KETINEEAA | B | | p24 | 71–80 | A*2501 (A25) | ETINEEAAEW | A, B, D | | p24 | 78–86 | B*4002 (B61) | AEWDRVHPV | B | | p24 | 84–92 | B7 | HPVHAGPIA | B, C, D, F | | p24 | 94–104 | B13 | GQMREPRGSDI | B, C | | p24 | 108–117 | B*5701 (B57) | TSTLQEQIGW | B, C | | p24 | 108–117 | B*5801 (B58) | TSTLQEQIGW | B, C | | p24 | 122–130 | B*3501 (B35) | PPIPVGDIY | A, B, C | | p24 | 128–135 | B*0801 (B8) | EIYKRWII | B | | p24 | 131–140 | B*2703 (B27) | RRWIQLGLQK | — | | p24 | 131–140 | B*2705 (B27) | KRWIILGLNK | A, B, C, D | | p24 | 137–145 | B*1501 (B62) | GLNKIVRMY | A, B | | p24 | 142–150 | Cw18 | VRMYSPVSI | B, C, F | | p24 | 143–150 | B*5201 (B52) | RMYSPTSI | B, F | | p24 | 161–169 | Cw18 | FRDYVDRFF | C | | p24 | 161–170 | B*1801 (B18) | FRDYVDRFYK | B, D | | p24 | 162–172 | A*2402 (A24) | RDYVDRFFKTL | A | | p24 | 162–172 | B*4402 (B44) | RDYVDRFYKTL | B, D | | p24 | 164–172 | Cw*0303 (Cw9) | YVDRFFKTL | A, C, D | | p24 | 164–172 | A*0207 (A2) | YVDRFYKTL | B | | p24 | 164–172 | B*1503 (B72) | YVDRFFKTL | A, C, D | | p24 | 164–172 | Cw*0304 (Cw10) | YVDRFFKTL | A, C, D | | p24 | 166–174 | B*1402 (B14) | DRFYKTLRA | B, D | | p24 | 174–184 | B*4402 (B44) | AEQASQDVKNW | B, C, D | | p24 | 174–185 | Cw5 | AEQASQEVKNWM | — | | p24 | 176–184 | B*5301 (B53) | QASQEVKNW | B, D | | p24 | 176–184 | B*5701 (B57) | QASQEVKNW | C | | p24 | 197–205 | B*0801 (B8) | DCKTILKAL | B | | p24 | 217–227 | A*1101 (A11) | ACQGVGGPGHK | B | | p24 | 223–231 | B*0702 (B7) | GPGHKARVL | B, C, D, F | | Protease | 3–11 | A*6802 (A68) | ITLWQRPLV | A, B, C, D | | Protease | 3–11 | A*7401 (A19) | ITLWQRPLV | A, B, C, D | | Protease | 30–38 | A*6802 (A68) | DTVLEEWNL | D | | Protease | 34–42 | B44 | EEMNLPGRW | B | | Protease | 57–66 | B13 | RQYDQILIEI | B | | Protease | 68–76 | B*1503 (B72) | GKKAIGTVL | BC | | Protease | 70–77 | B57 | KAIGTVLV | BC | | Protease | 76–84 | A*0201 (A2) | LVGPTPVNI | B | | Protease | 80–90 | B81 | TPVNIIGRNML | C | | Rev | 14–23 | B*5701 (B57) | KAVRLIKFLY | B | | Rev | 14–23 | B*5801 (B58) | KAVRLIKFLY | B | | Rev | 14–23 | B63 | KAVRLIKFLY | B | | Rev | 41–50 | B7 | RPAEPVPLQL | A, B, C, D, F | | Rev | 57–66 | A*0301 (A3) | ERILSTYLGR | B | | Rev | 67–75 | Cw*0501 | SAEPVPLQL | B | | RT | 5–12 | B*4001 (B60) | IETVPVKL | B | | RT | 18–26 | B*0801 (B8) | GPKVKQWPL | A, B, C, D | | RT | 33–41 | A*0201 (A2) | ALVEICTEM | B | | RT | 33–43 | A*0301 (A3) | ALVEICTEMEK | B | | RT | 42–50 | B*5101 (B51) | EKEGKISKI | B | | RT | 73–82 | A*0301 (A3) | KLVDFRELNK | B | | RT | 93–101 | A*0301 (A3) | GIPHPAGLK | B | | RT | 107–115 | B*3501 (B35) | TVLDVGDAY | AG, B | | RT | 118–127 | B*3501 (B35) | VPLDEDFRKY | B, C | | RT | 127–135 | A2 | YTAFTIPSV | — | | RT | 128–135 | B*5101 (B51) | TAFTIPSI | B | | RT | 137–146 | B18 | NETPGIRYQY | B, C | | RT | 142–149 | B*1401 (B14) | IRYQYNVL | C | | RT | 156–164 | B7 | SPAIFQSSM | A, B, C, D | | RT | 158–166 | A*0301 (A3) | AIFQSSMTK | A, B, C, D | | RT | 158–166 | A*1101 (A11) | AIFQSSMTK | — | | RT | 173–181 | A*3002 (A30) | KQNPDIVIY | B | | RT | 175–183 | B18 | NPEIVIYQY | C | | RT | 175–183 | B*3501 (B35) | HPDIVIYQY | A, B | | RT | 179–187 | A*0201 (A2) | VIYQYMDDL | A, B, C, D | | RT | 202–210 | B*4001 (B60) | IEELRQHLL | B | | RT | 244–252 | B*5701 (B57) | IVLPEKDSW | B | | RT | 260–271 | B*1501 (B62) | LVGKLNWASQIY | B | | RT | 263–271 | A*3002 (A30) | KLNWASQIY | B, C | | RT | 269–277 | A*0301 (A3) | QIYPGIKVR | B, C | | RT | 271–279 | B*4201 (B42) | YPGIKVRQL | B, C | | RT | 309–317 | A*0201 (A2) | ILKEPVHGV | A, B, C, D | | RT | 309–318 | B*1501 (B62) | ILKEPVHGVY | A, B, D | | RT | 333–341 | B13 | GQGQWTYQI | B | | RT | 341–350 | A*1101 (A11) | IYQEPFKNLK | B, C | | RT | 356–365 | A*3002 (A30) | RMRGAHTNDV | B | | RT | 356–366 | A*0301 (A3) | RMRGAHTNDVK | B | | RT | 375–383 | B*5801 (B58) | IAMESIVIW | B, C | | RT | 392–401 | A*3201 (A32) | PIQKETWETW | B | | RT | 436–445 | A*6802 (A68) | GAETFYVDGA | B, C | | RT | 438–448 | A66 | ETFYVDGAANR | B, C | | RT | 449–457 | A*2601 (A26) | ETKLGKAGY | B | | RT | 495–503 | Cw*0802 (Cw8) | IVTDSQYAL | — | | RT | 496–505 | B*1503 (B72) | VTDSQYALGI | — | | RT | 520–528 | A*1101 (A11) | QIIEQLIKK | B | | RT | 560–568 | B81 | LFLDGIDKA | — | | Tat | 2–11 | B*5301 (B53) | EPVDPRLEPW | B | | Tat | 2–11 | B58 | EPVDPRLEPW | B | | Tat | 30–37 | Cw12 | CCFHCQVC | B | | Tat | 38–47 | B*1503 (B72) | FQTKGLGISY | C | | Tat | 39–49 | A*6801 (A68) | ITKGLGISYGR | B | | Vif | 17–26 | A*0301 (A3) | RIRTWKSLVK | B | | Vif | 28–36 | A*0301 (A3) | HMYISKKAK | B | | Vif | 31–39 | B*5701 (B57) | ISKKAKGWF | B | | Vif | 48–57 | B*0702 (B7) | HPRVSSEVHI | B | | Vif | 57–66 | B51 | IPLGDAKLII | B | | Vif | 79–87 | B*1510 (B71) | WHLGHVSI | B | | Vif | 79–87 | B*3801 (B38) | WHLGQGVSI | B | | Vif | 102–111 | B*1801 (B18) | LADQLIHLHY | B | | Vif | 158–168 | A*0301 (A3) | KTKPPLPSVKK | B | | Vpr | 29–37 | B51 | EAVRHFPRI | B | | Vpr | 30–38 | B*5701 (B57) | AVRHFPRIW | B, C | | Vpr | 31–39 | B27 | VRHFPRIWL | B | | Vpr | 34–42 | B*0702 (B7) | FPRIWLHGL | B | | Vpr | 34–42 | B*8101 (B81) | FPRIWLHGL | B | | Vpr | 48–57 | A*6802 (A68) | ETYGDTWTGV | C | | Vpr | 52–62 | A*6801 (A68) | DTWAGVEAIIR | B | | Vpr | 59–67 | A*0201 (A2) | AIIRILQQL | B | | Vpu | 29–37 | A*3303 (A33) | EYRKILRQR | B | | Gag-Pol | 24–31 | Cw*0102 (Cw1) | NSPTRREL | — | | p2p7p1p6 | 1–10 | B*4501 (B45) | AEAMSQVTNS | — | | p2p7p1p6 | 42–50 | B14 | CRAPRKKGC | B | | p2p7p1p6 | 64–71 | B*4002 (B61) | TERQANFL | B | | p2p7p1p6 | 66–74 | B13 | RQANFLGKI | B, C | | p2p7p1p6 | 70–79 | A*0201 (A2) | FLGKIWPSYK | B | | p2p7p1p6 | 118–126 | B*4001 (B60) | KELYPLTSL | B |
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